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Biochemistry Student Companion : Principles of Biochemistry

Principles Of Biochemistry

Study Guide for Principles of Biochemistry

Principles of Biochemistry

Principles of Biochemistry

Summary

For one-semester introductory courses in Biochemistry. May be taught out of departments of chemistry, biology, or biochemistry. This concise, introductory text focuses on the basic principles of biochemistry, filling the gap between the encyclopedic volumes and the cursory overview texts. Widely praised in its previous edition for accuracy, currency, and clarity of exposition, the new edition has been thoroughly revised and updated to reflect recent changes in this dynamic discipline.

Table of Contents

PART ONE Introduction

Introduction to Biochemistry

3

(22)

Biochemistry Is a Modern Science

4

(1)

The Chemical Elements of Life

5

(3)

Many Important Biomolecules Are Polymers

8

(6)

Proteins

8

(1)

Polysaccharides

9

(1)

Nucleic Acids

10

(2)

Lipids and Membranes

12

(2)

The Energetics of Life

14

(1)

Biochemistry and Evolution

15

(1)

The Cell Is the Basic Unit of Life

15

(1)

Prokaryotic Cells: Structural Features

16

(1)

Eukaryotic Cells: Structural Features

17

(4)

The Nucleus

17

(2)

The Endoplasmic Reticulum and Golgi Apparatus

19

(1)

Mitochondria and Chloroplasts

19

(1)

Specialized Vesicles

20

(1)

The Cytoskeleton

21

(1)

A Picture of the Living Cell

21

(2)

Biochemistry Is Multidisciplinary

23

(2)

Appendix: The Special Terminology of Biochemistry

23

(1)

Selected Readings

24

(1)

Water

25

(26)

The Water Molecule Is Polar

26

(1)

Hydrogen Bonding in Water

27

(1)

Ionic and Polar Substances Dissolve in Water

28

(1)

Nonpolar Substances Are Insoluble in Water

29

(2)

Noncovalent Interactions in Biomolecules

31

(2)

Charge-Charge Interactions

31

(1)

Hydrogen Bonds

31

(1)

Van der Waals Forces

32

(1)

Hydrophobic Interactions

33

(1)

Water Is Nucleophilic

33

(2)

Ionization of Water

35

(1)

The pH Scale

36

(1)

Acid Dissociation Constants of Weak Acids

37

(3)

Buffered Solutions Resist Changes in pH

40

(11)

Summary

43

(1)

Problems

43

(2)

Selected Readings

45

(6)

PART TWO Structure and Function of Biomolecules

Amino Acids and the Primary Structures of Proteins

51

(30)

General Structure of Amino Acids

52

(3)

An Alternative Nomenclature

54

(1)

Structures of the 20 Common Amino Acids

55

(4)

Aliphatic R Groups

55

(1)

Aromatic R Groups

56

(1)

Sulfur-Containing R Groups

57

(1)

Side Chains with Alcohol Groups

57

(1)

Basic R Groups

58

(1)

Acidic R Groups and Their Amide Derivatives

58

(1)

The Hydrophobicity of Amino Acid Side Chains

58

(1)

Other Amino Acids and Amino Acid Derivatives

59

(1)

Ionization of Amino Acids

60

(4)

Peptide Bonds Link Amino Acids in Proteins

64

(2)

Protein Purification Techniques

66

(3)

Amino Acid Composition of Proteins

69

(1)

Determining the Sequence of Amino Acid Residues

70

(3)

Protein Sequencing Strategies

73

(4)

Comparisons of the Primary Structures of Proteins Reveal Evolutionary Relationships

77

(4)

Summary

78

(1)

Problems

79

(1)

Selected Readings

80

(1)

Proteins: Three-Dimensional Structure and Function

81

(49)

There Are Four Levels of Protein Structure

83

(1)

Methods for Determining Protein Structure

84

(2)

The Conformation of the Peptide Group

86

(3)

The α Helix

89

(3)

β Strands and β Sheets

92

(2)

Loops and Turns

94

(2)

Tertiary Structure of Proteins

96

(6)

Supersecondary Structures

96

(1)

Domains

97

(5)

Domain Structure and Function

102

(1)

Quaternary Structure

102

(2)

Protein Denaturation and Renaturation

104

(3)

Protein Folding and Stability

107

(5)

The Hydrophobic Effect

107

(2)

Hydrogen Bonding

109

(1)

Van der Waals Interactions and Charge-Charge Interactions

110

(1)

Protein Folding Is Assisted by Chaperones

110

(2)

Collagen, a Fibrous Protein

112

(2)

Structures of Myoglobin and Hemoglobin

114

(2)

Oxygen Binding to Myoglobin and Hemoglobin

116

(5)

Oxygen Binds Reversibly to Heme

116

(1)

Oxygen-Binding Curves of Myoglobin and Hemoglobin

117

(2)

Hemoglobin Is an Allosteric Protein

119

(2)

Antibodies Bind Specific Antigens

121

(9)

Summary

124

(1)

Problems

125

(2)

Selected Readings

127

(3)

Properties of Enzymes

130

(32)

The Six Classes of Enzymes

131

(2)

Kinetic Experiments Reveal Enzyme Properties

133

(2)

Chemical Kinetics

133

(1)

Enzyme Kinetics

134

(1)

The Michaelis-Menten Equation

135

(4)

Derivation of the Michaelis-Menten Equation

137

(1)

The Meanings of Km

138

(1)

Kinetic Constants Indicate Enzyme Activity and Specificity

139

(1)

Measurement of Km and Vmax

140

(1)

Kinetics of Multisubstrate Reactions

141

(1)

Reversible Enzyme Inhibition

142

(5)

Competitive Inhibition

143

(2)

Uncompetitive Inhibition

145

(1)

Noncompetitive Inhibition

146

(1)

Uses of Enzyme Inhibition

146

(1)

Irreversible Enzyme Inhibition

147

(1)

Site-Directed Mutagenesis Modifies Enzymes

148

(1)

Regulation of Enzyme Activity

148

(7)

Phosphofructokinase Is an Allosteric Enzyme

149

(1)

General Properties of Allosteric Enzymes

150

(2)

Two Theories of Allosteric Regulation

152

(2)

Regulation by Covalent Modification

154

(1)

Multienzyme Complexes and Multifunctional Enzymes

155

(7)

Summary

156

(1)

Problems

156

(3)

Selected Readings

159

(3)

Mechanisms of Enzymes

162

(35)

The Terminology of Mechanistic Chemistry

162

(2)

Catalysts Stabilize Transition States

164

(2)

Chemical Modes of Enzymatic Catalysis

166

(4)

Polar Amino Acid Residues in Active Sites

166

(1)

Acid-Base Catalysis

167

(1)

Covalent Catalysis

168

(1)

pH Affects Enzymatic Rates

169

(1)

Diffusion-Controlled Reactions

170

(4)

Triose Phosphate Isomerase

171

(2)

Superoxide Dismutase

173

(1)

Binding Modes of Enzymatic Catalysis

174

(6)

The Proximity Effects

175

(2)

Weak Binding of Substrates to Enzymes

177

(1)

Transition-State Stabilization

178

(2)

Induced Fit

180

(2)

Lysozyme Binds an Ionic Intermediate Tightly

182

(3)

Proposed Transition State for a Bimolecular Reaction

185

(1)

Properties of Serine Proteases

185

(12)

Zymogens Are Inactive Enzyme Precursors

186

(1)

Substrate Specificity of Serine Proteases

187

(1)

Serine Proteases Use Both the Chemical and the Binding Modes of Catalysis

188

(4)

Summary

192

(1)

Problems

193

(2)

Selected Readings

195

(2)

Coenzymes and Vitamins

197

(34)

Many Enzymes Require Inorganic Cations

198

(1)

Coenzyme Classification

199

(4)

Metabolite Coenzymes

199

(1)

Nucleosides and Nucleotides

200

(2)

Vitamin-Derived Coenzymes and Nutrition

202

(1)

Vitamin C: A Vitamin but Not a Coenzyme

202

(1)

NAD&angst; and NADP&angst;

203

(4)

NAD Binding to Dehydrogenases

206

(1)

FAD and FMN

207

(4)

An FAD-Requiring Hydroxylase That Has a Unique Test for Its Proper Substrate